MA-CA-SP molecular dynamics trajectory for HIV-1 Gag protein

MA-CA-SP1_trajectory.tar.gz is a compressed folder containing files md_0_1.gro and md_0_1.xtc that correspond to a molecular dynamics trajectory of 50 ns for MA-CA-SP1. This model includes amino acids 2 to 377 of protein GAG-HIV1 (UNIPROT code P12497) in a compact conformation.md.mdp is a text file with the conditions to generate the molecular dynamics run. The simulation was performed using the GROMACS package version 2018.1 (Abraham et al., 2015) in conjunction with the GROMOS 53A6 force field (Oostenbrink et al., 2004). Water was represented explicitly using the SPC/E model (Berendsen et al.,1987). The system was simulated under periodic conditions in a dodecahedron box. The temperature was maintained throughout the simulation by independently coupling the protein and the solvent to an external temperature bath at 310 K with a coupling constant tau_t= 0.1 ps using a modified Berendsen thermostat (Bussi et al., 2007). The pressure was maintained at 1 bar by weakly coupling the system to an isotropic pressure bath (Parrinello & Rahman., 1981) using an isothermal compressibility of 4.5 x 10-5 bar-1 and a coupling constant of tau_p= 2.0 ps. During the simulations, the length of all bonds within the protein was constrained using the LINear Constraint Solver (LINCS) algorithm (Hess et al. 1997). All bonds, even heavy atom-H bonds were constrained. The time step for integrating the equations of motion was 2 fs. The algorithm used for computing long range electrostatic interactions was Particle-Mesh-Ewald (PME) (Petersen et al. 1995). Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., Lindahl, E. (2015) SoftwareX 1–2:19–25. Berendsen, H. J. C., Postma, J. P .M., and van Gunsteren, W. F., DiNola, A., Haak, J. R. (1984). J. Chem. pHYS. 81, 3684-3690. Bussi, G., Donadio, D., Parrinello, M., (2007). J. Chem. Phys. 126, 014101-7. Hess, B., Bekker, H.,Berendsen, H.J.C., and Fraaijc, J. G.E.M. (1997). J. Comput. Chem. 18, 1463-1472. Oostenbrink B.C., Pitera J.W., Lipzig M.M.H., Meerman J.H.N., Gunsteren W.F. van (2000) J. Comput. Chem. 25:1656-1676. Parrinello, M. and Rahman, A. (1981). J. Appl. Phys. 52, 7182-7190. Petersen H. G. (1995) J. Chem. Phys. 103, 3668-3679.MA-CA-SP1_trajectory.tar.gz 是一款压缩文件夹，内含md_0_1.gro与md_0_1.xtc文件，对应MA-CA-SP1的50纳秒分子动力学轨迹。该模型包含蛋白GAG-HIV1（UNIPROT编号P12497）的第2至377位氨基酸，处于紧凑构象。 md.mdp是一份记录分子动力学运行参数的文本文件。本模拟采用GROMACS 2018.1版本软件包（Abraham等人，2015）结合GROMOS 53A6力场（Oostenbrink等人，2004）完成。溶剂水采用SPC/E模型显式表示（Berendsen等人，1987）。 体系在十二面体周期性边界条件下开展模拟。通过将蛋白与溶剂分别耦合至310 K的外部恒温浴，采用改进型Berendsen恒温器（Bussi等人，2007），耦合常数τ_t=0.1 ps，维持模拟全程温度恒定。通过将体系弱耦合至各向同性恒压浴（Parrinello与Rahman，1981），设置等温压缩率为4.5×10⁻⁵ bar⁻¹，耦合常数τ_p=2.0 ps，将体系压力维持在1 bar。 模拟过程中，采用线性约束求解器（LINear Constraint Solver, LINCS）算法（Hess等人，1997）约束蛋白内所有化学键的长度，包括重原子与氢原子形成的化学键。运动方程积分的时间步长为2 fs。长程静电相互作用的计算采用粒子网格埃wald（Particle-Mesh-Ewald, PME）算法（Petersen等人，1995）。 参考文献如下： Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., Lindahl, E. (2015) SoftwareX 1–2:19–25. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., Haak, J. R. (1984). The Journal of Chemical Physics 81, 3684-3690. Bussi, G., Donadio, D., Parrinello, M. (2007). The Journal of Chemical Physics 126, 014101-7. Hess, B., Bekker, H., Berendsen, H. J. C., and Fraaijc, J. G. E. M. (1997). Journal of Computational Chemistry 18, 1463-1472. Oostenbrink, B. C., Pitera, J. W., Lipzig, M. M. H., Meerman, J. H. N., van Gunsteren, W. F. (2000) Journal of Computational Chemistry 25:1656-1676. Parrinello, M. and Rahman, A. (1981). Journal of Applied Physics 52, 7182-7190. Petersen, H. G. (1995) The Journal of Chemical Physics 103, 3668-3679.